Yes, Vuescan and Nikon Scan (both at default settings) will get different raw data (I did apply the same gamma correction to all of them otherwise it would much harder for us humans to see the difference) from the negative (for scanners with independent RGB exposure). I don't have any Nikon scanner anymore so I can't demonstrate that, but I can show you the difference in raw data between Vuescan's 'Color Negative film' and 'Slide film' input type:
Slide film:
Color negative film:
As you can see, when in 'Color negative film' mode Vuescan will slightly lower the exposure for R channel, increase exposure for G and even more for B channel. That somewhat aligns R, G and B channels and in effect removes some of the orange mask which in theory could benefit scanners with lower dynamic range.
Now, Nikon Scan would do something like this:
In theory, yes. But sensor dynamic range and 16bit signal processing in Nikon CS 9000 should make that advantage negligible. Personally, I avoid scanning in Color negative mode since longer exposure means that film will get more heat and curl more. This is not a concern if you scan in glass holder, or course.
Yes, Vuescan's equivalent is RGB exposure setting (plus individual R, G and B) which is automatically set by Vuescan depending on the preview scan analysis and film type mode. The difference between Nikon Scan and Vuescan with this settings is that by default Vuescan will change exposure and Nikon Scan will not and you have to do it yourself.
Not Vuescan response. CCD sensor response. At least that is my explanation for why the effects is more visible with scanning in Vuescan. Since scanners do not get higher/lower exposure by altering light source brightness, but by the time the sensor's shutter is open there should not be a case when more light means more reflections. It's either that or there is some post-processing for that problem in Nikon Scan, but I doubt that is the case.